Human Gene MCCC1 (ENST00000265594.9_7) from GENCODE V47lift37
  Description: methylcrotonyl-CoA carboxylase subunit 1, transcript variant 1 (from RefSeq NM_020166.5)
Gencode Transcript: ENST00000265594.9_7
Gencode Gene: ENSG00000078070.14_12
Transcript (Including UTRs)
   Position: hg19 chr3:182,733,006-182,817,284 Size: 84,279 Total Exon Count: 19 Strand: -
Coding Region
   Position: hg19 chr3:182,733,226-182,817,228 Size: 84,003 Coding Exon Count: 19 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:182,733,006-182,817,284)mRNA (may differ from genome)Protein (725 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: MCCA_HUMAN
DESCRIPTION: RecName: Full=Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial; Short=MCCase subunit alpha; EC=6.4.1.4; AltName: Full=3-methylcrotonyl-CoA carboxylase 1; AltName: Full=3-methylcrotonyl-CoA carboxylase biotin-containing subunit; AltName: Full=3-methylcrotonyl-CoA:carbon dioxide ligase subunit alpha; Flags: Precursor;
CATALYTIC ACTIVITY: ATP + 3-methylcrotonoyl-CoA + HCO(3)(-) = ADP + phosphate + 3-methylglutaconyl-CoA.
COFACTOR: Biotin.
PATHWAY: Amino-acid degradation; L-leucine degradation; (S)-3- hydroxy-3-methylglutaryl-CoA from 3-isovaleryl-CoA: step 2/3.
SUBUNIT: Probably a dodecamer composed of six biotin-containing alpha subunits and six beta subunits.
SUBCELLULAR LOCATION: Mitochondrion matrix.
DISEASE: Defects in MCCC1 are the cause of methylcrotonoyl-CoA carboxylase 1 deficiency (MCC1D) [MIM:210200]. An autosomal recessive disorder of leucine catabolism. The phenotype is variable, ranging from neonatal onset with severe neurological involvement to asymptomatic adults. There is a characteristic organic aciduria with massive excretion of 3-hydroxyisovaleric acid and 3-methylcrotonylglycine, usually in combination with a severe secondary carnitine deficiency.
SIMILARITY: Contains 1 ATP-grasp domain.
SIMILARITY: Contains 1 biotin carboxylation domain.
SIMILARITY: Contains 1 biotinyl-binding domain.
SEQUENCE CAUTION: Sequence=BAD92974.1; Type=Erroneous initiation;
WEB RESOURCE: Name=GeneReviews; URL="http://www.ncbi.nlm.nih.gov/sites/GeneTests/lab/gene/MCCC1";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: MCCC1
Diseases sorted by gene-association score: 3-methylcrotonyl-coa carboxylase 1 deficiency* (1200), 3-methylcrotonyl-coa carboxylase deficiency* (379), mccc1-related 3-methylcrotonyl-coa carboxylase deficiency* (100), ketothiolase deficiency (10), multiple carboxylase deficiency (7)
* = Manually curated disease association

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 15.94 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 427.24 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -19.5056-0.348 Picture PostScript Text
3' UTR -49.00220-0.223 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011761 - ATP-grasp
IPR013815 - ATP_grasp_subdomain_1
IPR013816 - ATP_grasp_subdomain_2
IPR001882 - Biotin_BS
IPR011764 - Biotin_carboxylation_dom
IPR005482 - Biotin_COase_C
IPR000089 - Biotin_lipoyl
IPR005481 - CarbamoylP_synth_lsu_N
IPR005479 - CbamoylP_synth_lsu-like_ATP-bd
IPR016185 - PreATP-grasp_fold
IPR011054 - Rudment_hybrid_motif
IPR011053 - Single_hybrid_motif

Pfam Domains:
PF00289 - Biotin carboxylase, N-terminal domain
PF00364 - Biotin-requiring enzyme
PF02222 - ATP-grasp domain
PF02655 - ATP-grasp domain
PF02785 - Biotin carboxylase C-terminal domain
PF02786 - Carbamoyl-phosphate synthase L chain, ATP binding domain
PF07478 - D-ala D-ala ligase C-terminus
PF08443 - RimK-like ATP-grasp domain

SCOP Domains:
51230 - Single hybrid motif
51246 - Rudiment single hybrid motif
52440 - PreATP-grasp domain
56059 - Glutathione synthetase ATP-binding domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2EJM - NMR MuPIT


ModBase Predicted Comparative 3D Structure on Q96RQ3
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0004075 biotin carboxylase activity
GO:0004485 methylcrotonoyl-CoA carboxylase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0009374 biotin binding
GO:0016874 ligase activity
GO:0046872 metal ion binding

Biological Process:
GO:0006552 leucine catabolic process
GO:0006768 biotin metabolic process
GO:0051291 protein heterooligomerization

Cellular Component:
GO:0002169 3-methylcrotonyl-CoA carboxylase complex, mitochondrial
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:1905202 methylcrotonoyl-CoA carboxylase complex


-  Descriptions from all associated GenBank mRNAs
  BC004187 - Homo sapiens methylcrotonoyl-Coenzyme A carboxylase 1 (alpha), mRNA (cDNA clone MGC:2822 IMAGE:2964422), complete cds.
BC004214 - Homo sapiens methylcrotonoyl-Coenzyme A carboxylase 1 (alpha), mRNA (cDNA clone MGC:4495 IMAGE:2964422), complete cds.
AF297332 - Homo sapiens 3-methylcrotonyl-CoA carboxylase biotin-containing subunit (MCCA) mRNA, complete cds.
BC036395 - Homo sapiens methylcrotonoyl-Coenzyme A carboxylase 1 (alpha), mRNA (cDNA clone IMAGE:5259867).
AK098411 - Homo sapiens cDNA FLJ25545 fis, clone JTH01447, highly similar to Homo sapiens MCC-B mRNA for 3-methylcrotonyl-CoA carboxylase biotin-containing subunit.
CR749608 - Homo sapiens mRNA; cDNA DKFZp686B20267 (from clone DKFZp686B20267).
AK023051 - Homo sapiens cDNA FLJ12989 fis, clone NT2RP3000085, moderately similar to ACETYL-/PROPIONYL-COENZYME A CARBOXYLASE ALPHA CHAIN [CONTAINS: BIOTIN CARBOXYLASE (EC 6.3.4.14); BIOTIN CARBOXYL CARRIER PROTEIN (BCCP)].
AB029826 - Homo sapiens MCC-B mRNA for 3-methylcrotonyl-CoA carboxylase biotin-containing subunit, complete cds.
AF310339 - Homo sapiens 3-methylcrotonyl-CoA carboxylase alpha subunit (MCCA) mRNA, complete cds.
AF310972 - Homo sapiens 3-methylcrotonyl-CoA carboxylase alpha subunit (MCCA) mRNA, complete cds.
BC042453 - Homo sapiens methylcrotonoyl-Coenzyme A carboxylase 1 (alpha), mRNA (cDNA clone IMAGE:4838744), with apparent retained intron.
AL442091 - Homo sapiens mRNA; cDNA DKFZp547H017 (from clone DKFZp547H017).
JD487046 - Sequence 468070 from Patent EP1572962.
JD117964 - Sequence 98988 from Patent EP1572962.
AB209737 - Homo sapiens mRNA for methylcrotonoyl-Coenzyme A carboxylase 1 (alpha) variant protein.
JD525110 - Sequence 506134 from Patent EP1572962.
JD385366 - Sequence 366390 from Patent EP1572962.
JD361671 - Sequence 342695 from Patent EP1572962.
JD236481 - Sequence 217505 from Patent EP1572962.
JD342860 - Sequence 323884 from Patent EP1572962.
KJ899268 - Synthetic construct Homo sapiens clone ccsbBroadEn_08662 MCCC1 gene, encodes complete protein.
KR710012 - Synthetic construct Homo sapiens clone CCSBHm_00008924 MCCC1 (MCCC1) mRNA, encodes complete protein.
KR710013 - Synthetic construct Homo sapiens clone CCSBHm_00008926 MCCC1 (MCCC1) mRNA, encodes complete protein.
KR710014 - Synthetic construct Homo sapiens clone CCSBHm_00008930 MCCC1 (MCCC1) mRNA, encodes complete protein.
KR710015 - Synthetic construct Homo sapiens clone CCSBHm_00008938 MCCC1 (MCCC1) mRNA, encodes complete protein.
KU178727 - Homo sapiens methylcrotonoyl-CoA carboxylase 1 isoform 1 (MCCC1) mRNA, partial cds.
KU178728 - Homo sapiens methylcrotonoyl-CoA carboxylase 1 isoform 2 (MCCC1) mRNA, complete cds, alternatively spliced.
AB587379 - Synthetic construct DNA, clone: pF1KB5080, Homo sapiens MCCC1 gene for methylcrotonoyl-Coenzyme A carboxylase 1, without stop codon, in Flexi system.
AK294882 - Homo sapiens cDNA FLJ54709 complete cds, highly similar to Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial precursor (EC 6.4.1.4).
AK295293 - Homo sapiens cDNA FLJ53328 complete cds, highly similar to Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial precursor (EC 6.4.1.4).
JD019496 - Sequence 520 from Patent EP1572962.
AK316428 - Homo sapiens cDNA, FLJ79327 complete cds, highly similar to Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial precursor (EC 6.4.1.4).
CU678606 - Synthetic construct Homo sapiens gateway clone IMAGE:100017786 5' read MCCC1 mRNA.

-  Biochemical and Signaling Pathways
  BioCyc Knowledge Library
LEU-DEG2-PWY - L-leucine degradation

Reactome (by CSHL, EBI, and GO)

Protein Q96RQ3 (Reactome details) participates in the following event(s):

R-HSA-2993799 HLCS biotinylates 6xMCCC1:6xMCCC2
R-HSA-70773 beta-methylcrotonyl-CoA + ATP + CO2 <=> beta-methylglutaconyl-CoA + ADP + orthophosphate + H2O [MCCA]
R-HSA-508308 beta-methylglutaconyl-CoA + ADP + orthophosphate + H2O <=> beta-methylcrotonyl-CoA + ATP + CO2 [MCCA]
R-HSA-196780 Biotin transport and metabolism
R-HSA-3371599 Defective HLCS causes multiple carboxylase deficiency
R-HSA-70895 Branched-chain amino acid catabolism
R-HSA-196849 Metabolism of water-soluble vitamins and cofactors
R-HSA-3323169 Defects in biotin (Btn) metabolism
R-HSA-71291 Metabolism of nitrogenous molecules
R-HSA-196854 Metabolism of vitamins and cofactors
R-HSA-3296482 Defects in vitamin and cofactor metabolism
R-HSA-1430728 Metabolism
R-HSA-5668914 Diseases of metabolism
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000265594.1, ENST00000265594.2, ENST00000265594.3, ENST00000265594.4, ENST00000265594.5, ENST00000265594.6, ENST00000265594.7, ENST00000265594.8, MCCA, MCCA_HUMAN, NM_020166, Q59ES4, Q96RQ3, Q9H959, Q9NS97, uc317icm.1, uc317icm.2
UCSC ID: ENST00000265594.9_7
RefSeq Accession: NM_020166.5
Protein: Q96RQ3 (aka MCCA_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.